Repository logo

Infoscience

  • English
  • French
Log In
Logo EPFL, École polytechnique fédérale de Lausanne

Infoscience

  • English
  • French
Log In
  1. Home
  2. Academic and Research Output
  3. Journal articles
  4. Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
 
research article

Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding

Abriata, Luciano A.
•
Dal Peraro, Matteo  
2015
Scientific Reports

Protein-protein recognition and binding are governed by diffusion, noncovalent forces and conformational flexibility, entangled in a way that only molecular dynamics simulations can dissect at high resolution. Here we exploited ubiquitin's noncovalent dimerization equilibrium to assess the potential of atomistic simulations to reproduce reversible protein-protein binding, by running submicrosecond simulations of systems with multiple copies of the protein at millimolar concentrations. The simulations essentially fail because they lead to aggregates, yet they reproduce some specificity in the binding interfaces as observed in known covalent and noncovalent ubiquitin dimers. Following similar observations in literature we hint at electrostatics and water descriptions as the main liable force field elements, and propose that their optimization should consider observables relevant to multi-protein systems and unfolded proteins. Within limitations, analysis of binding events suggests salient features of protein-protein recognition and binding, to be retested with improved force fields. Among them, that specific configurations of relative direction and orientation seem to trigger fast binding of two molecules, even over 50 angstrom distances; that conformational selection can take place within surface-to-surface distances of 10 to 40 angstrom i.e. well before actual intermolecular contact; and that establishment of contacts between molecules further locks their conformations and relative orientations.

  • Files
  • Details
  • Metrics
Type
research article
DOI
10.1038/srep10549
Web of Science ID

WOS:000355588500001

Author(s)
Abriata, Luciano A.
Dal Peraro, Matteo  
Date Issued

2015

Publisher

Nature Publishing Group

Published in
Scientific Reports
Volume

5

Article Number

10549

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
UPDALPE  
Available on Infoscience
September 28, 2015
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/119361
Logo EPFL, École polytechnique fédérale de Lausanne
  • Contact
  • infoscience@epfl.ch

  • Follow us on Facebook
  • Follow us on Instagram
  • Follow us on LinkedIn
  • Follow us on X
  • Follow us on Youtube
AccessibilityLegal noticePrivacy policyCookie settingsEnd User AgreementGet helpFeedback

Infoscience is a service managed and provided by the Library and IT Services of EPFL. © EPFL, tous droits réservés